Extra security measures have been put in place at the complex after a recent attack
Three Palestinians have been killed in east Jerusalem near to the Old City where Israeli forces have clashed with Muslim worshippers, the Palestinian health ministry said.
One victim was shot dead and a 17-year-old was also killed, according to a hospital spokesman and the ministry.
Details of the third death are currently unclear.
The violence erupted over a ban on Muslim men under the age of 50 entering the al Aqsa mosque and the installation of metal detectors.
There have been almost daily clashes between Israeli officers and Palestinians at the entrances to the site - considered sacred by both Muslims and Jews.
Protesters on Friday ran for cover from tear gas as tensions continued to rise amid an ongoing dispute over access.
Israeli forces used tear gas, water cannon and rubber bullets to try to disperse crowds hurling stones and bottles.
Palestinian authorities claimed live ammunition was also used.
Four officers were hurt in the violence, said the Israeli military.
Extra security measures were put in place at the complex - known as the Temple Mount by Jews and the Noble Sanctuary by Muslims - after three Arab Israelis attacked a patrol near Lion's Gate a week ago, killing two policemen.
The three attackers, from the city of Umm al Fahm, were all killed by Israeli security forces.
Religious clerics from the Waqf - the Jordanian trust which manages the site - called for mass protests at Friday noon prayers.
They asked every mosque in the city to close and worshippers were urged to instead pray outside the gates of al Aqsa rather than submit to the security procedures.
"Entry to the Old City and Temple Mount will be limited to men aged 50 and over. Women of all ages will be permitted," an Israeli police statement said.
Spokesman Micky Rosenfeld said 3,000 members of the security forces had been deployed to the area.
Access to the compound is already difficult - or impossible - for many Palestinians.
Under the status quo - which dates back to the Ottoman period - only Muslims have the right to worship on the plaza, although Jews and people from other faiths can visit.
Different residency rights have been introduced by Israel since it captured the West Bank, Gaza and East Jerusalem in the 1967 Six-Day War.
Since Israel captured the Old City it has remained committed to that formula.
However, Palestinians claim the extra security measures represent a change and a further erosion of their rights to access to the holy site.
Every night for the last week Palestinians have been refusing to go through the metal detectors and have instead been conducting prayers on the street.
Israel asserts there is no change to the status quo and that the metal detectors are necessary to stop further attacks.